Summary of Study ST000929
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR000643. The data can be accessed directly via it's Project DOI: 10.21228/M8JT38 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.
| Study ID | ST000929 |
| Study Title | Metabolomics Analysis of Aqueous Humour in the Presence of Glaucoma Drainage Devices |
| Study Type | Metabolomics Evaluation of Aqueous Humor Samples from Left (treated) and Right (Control) Eyes of Rabbits. |
| Study Summary | Metabolomic experiments were carried out on aqueous humor samples provided by Ramesh Ayyala. Through this collaboration, we propose to study aqueous humor from control and experimental rabbits to better understand metabolic differences in the aqueous humor samples. |
| Institute | University of North Carolina |
| Department | Nutrition Research Institute |
| Laboratory | ERCMRC |
| Last Name | Sumner |
| First Name | Susan |
| Address | 500 Laureate Way, Kannapolis, NC, 28081, USA |
| susan_sumner@unc.edu | |
| Phone | 7042505066 |
| Submit Date | 2018-02-11 |
| Num Groups | 9 |
| Total Subjects | 56 |
| Num Males | 56 |
| Analysis Type Detail | LC-MS |
| Release Date | 2018-12-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000643 |
| Project DOI: | doi: 10.21228/M8JT38 |
| Project Title: | Metabolomics Analysis of Aqueous Humour in the Presence of Glaucoma Drainage Devices |
| Project Type: | Metabolomics of the aqueous humor of rabbits with Ahmed Glaucoma Valve implantation. |
| Project Summary: | Aqueous humor samples for metabolomics experiment were generated in the following manner: Eight adult male white rabbits were given seven days to acclimate to their environment. On day eight, an Ahmed Glaucoma Valve was implanted into the left eye of every rabbit. The un-operated right eye served as control. One rabbit was lost during the course of the study. After adequate anesthesia, aqueous humor samples were taken from both eyes of each rabbit before surgery (A samples), and at 27 (B samples), 52 (C samples) and 153 days (IV samples) after surgery. |
| Institute: | Tulane University School of Medicine |
| Department: | Ophthalmology |
| Last Name: | Ayyala |
| First Name: | Ramesh S. |
| Address: | 1430 Tulane Ave., New Orleans, LA 70112 |
| Email: | rayyala@tulane.edu |
| Phone: | 504-998-2261 |
Subject:
| Subject ID: | SU000968 |
| Subject Type: | Mammal |
| Subject Species: | Oryctolagus cuniculus |
| Taxonomy ID: | 9986 |
| Gender: | Male |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Oryctolagus cuniculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Eye | Treatment |
|---|---|---|---|
| SA055443 | Day153_IV-60L_POS | Left Eye | 153 days post-valve implantation |
| SA055444 | Day153_IV-59L_POS | Left Eye | 153 days post-valve implantation |
| SA055445 | Day153_IV-61L_POS | Left Eye | 153 days post-valve implantation |
| SA055446 | Day153_IV-62L_POS | Left Eye | 153 days post-valve implantation |
| SA055447 | Day153_IV-64L_POS | Left Eye | 153 days post-valve implantation |
| SA055448 | Day153_IV-58L_POS | Left Eye | 153 days post-valve implantation |
| SA055449 | Day153_IV-65L_POS | Left Eye | 153 days post-valve implantation |
| SA055450 | Day27_L-X60-B_POS | Left Eye | 27 days post-valve implantation |
| SA055451 | Day27_L-X59-B_POS | Left Eye | 27 days post-valve implantation |
| SA055452 | Day27_L-X62-B_POS | Left Eye | 27 days post-valve implantation |
| SA055453 | Day27_L-X64-B_POS | Left Eye | 27 days post-valve implantation |
| SA055454 | Day27_L-X65-B_POS | Left Eye | 27 days post-valve implantation |
| SA055455 | Day27_L-X58-B_POS | Left Eye | 27 days post-valve implantation |
| SA055456 | Day27_L-X61-B_POS | Left Eye | 27 days post-valve implantation |
| SA055457 | Day52_L-60-C_POS | Left Eye | 52 days post-valve implantation |
| SA055458 | Day52_L-58-C_POS | Left Eye | 52 days post-valve implantation |
| SA055459 | Day52_L-65-C_POS | Left Eye | 52 days post-valve implantation |
| SA055460 | Day52_L-61-C_POS | Left Eye | 52 days post-valve implantation |
| SA055461 | Day52_L-59-C_POS | Left Eye | 52 days post-valve implantation |
| SA055462 | Day52_L-62-C_POS | Left Eye | 52 days post-valve implantation |
| SA055463 | Day52_L-64-C_POS | Left Eye | 52 days post-valve implantation |
| SA055464 | Day52_L-63-C_POS | Left Eye | 52 days post-valve implantation |
| SA055465 | R_Pool_A2_POS | Pool from aqueous humor from control (right) eyes before surgery in the left eye. | pre-valve implantation |
| SA055466 | R_Pool_A3_POS | Pool from aqueous humor from control (right) eyes before surgery in the left eye. | pre-valve implantation |
| SA055467 | R_Pool_A1_POS | Pool from aqueous humor from control (right) eyes before surgery in the left eye. | pre-valve implantation |
| SA055468 | L_Pool_A2_POS | Pool from aqueous humor from treated (left) eyes before valve implantation. | pre-valve implantation |
| SA055469 | L_Pool_A1_POS | Pool from aqueous humor from treated (left) eyes before valve implantation. | pre-valve implantation |
| SA055470 | L_Pool_A3_POS | Pool from aqueous humor from treated (left) eyes before valve implantation. | pre-valve implantation |
| SA055471 | C_IV-58R_POS | Right Eye | control- 153 days post-valve |
| SA055472 | C_IV-65R_POS | Right Eye | control- 153 days post-valve |
| SA055473 | C_IV-60R_POS | Right Eye | control- 153 days post-valve |
| SA055474 | C_IV-64R_POS | Right Eye | control- 153 days post-valve |
| SA055475 | C_IV-59R_POS | Right Eye | control- 153 days post-valve |
| SA055476 | C_IV-62R_POS | Right Eye | control- 153 days post-valve |
| SA055477 | C_IV-61R_POS | Right Eye | control- 153 days post-valve |
| SA055478 | C_R-X59-B_POS | Right Eye | control- 27 days post-valve |
| SA055479 | C_R-X60-B_POS | Right Eye | control- 27 days post-valve |
| SA055480 | C_R-X61-B_POS | Right Eye | control- 27 days post-valve |
| SA055481 | C_R-X64-B_POS | Right Eye | control- 27 days post-valve |
| SA055482 | C_R-X58-B_POS | Right Eye | control- 27 days post-valve |
| SA055483 | C_R-X65-B_POS | Right Eye | control- 27 days post-valve |
| SA055484 | C_R-X62-B_POS | Right Eye | control- 27 days post-valve |
| SA055485 | C_R-60-C_POS | Right Eye | control- 52 days post-valve |
| SA055486 | C_R-63-C_POS | Right Eye | control- 52 days post-valve |
| SA055487 | C_R-61-C_POS | Right Eye | control- 52 days post-valve |
| SA055488 | C_R-64-C_POS | Right Eye | control- 52 days post-valve |
| SA055489 | C_R-65-C_POS | Right Eye | control- 52 days post-valve |
| SA055490 | C_R-62-C_POS | Right Eye | control- 52 days post-valve |
| SA055491 | C_R-59-C_POS | Right Eye | control- 52 days post-valve |
| SA055492 | C_R-58-C_POS | Right Eye | control- 52 days post-valve |
| SA055493 | Pool_1_POS | Total Pool | Whole Study QC Pool _1 |
| SA055494 | Pool_2_POS | Total Pool | Whole Study QC Pool _2 |
| SA055495 | Pool_3_POS | Total Pool | Whole Study QC Pool _3 |
| SA055496 | Pool_4_POS | Total Pool | Whole Study QC Pool _4 |
| SA055497 | Pool_5_POS | Total Pool | Whole Study QC Pool _5 |
| SA055498 | Pool_6_POS | Total Pool | Whole Study QC Pool _6 |
| Showing results 1 to 56 of 56 |
Collection:
| Collection ID: | CO000962 |
| Collection Summary: | Aqueous humor was collected from both eyes before surgery, then at one month, two months, and five months post operatively. After adequate anesthesia the eye was prepped with 5% betadine solution and then covered with a sterile drape. A sterile 27G needle was inserted into the anterior chamber through the clear cornea of the para-limbal area. Approximately 0.1 ml of aqueous humor was acquired in each collection cycle. The samples were immediately placed over an ice bath then transferred to a freezer for storage at -70ºC. |
| Sample Type: | aqueous humour |
Treatment:
| Treatment ID: | TR000982 |
| Treatment Summary: | A Glaucoma Drainage Device was inserted into the left eye of each of Eight Rabbits. Aqueous humor was collected from the left (treated) eye and right (control) eye before implantation and at several time points after surgey. |
Sample Preparation:
| Sampleprep ID: | SP000975 |
| Sampleprep Summary: | Whole Study Pooled QC Thawed aqueous humor samples on ice. Whole study pooled QC samples were created by combining 10 µL aliquot from each of the study samples (Time Points B, C and D) into a 2 mL Lo-Bind eppendorf tube. The QC pooled sample was then vortexed for 30 seconds. Time Point A Pools Aqueous humor samples were collected from both, right and left, eyes and provided for metabolomics analysis. Aqueous humor from the right eyes from experiment A were combined into a 2 mL Lo-Bind Eppendorf tube to make a right eye pool from experiment A. This same procedure was repeated to make a pool from the left eye aqueous humor from experiment A. The two time point A pools were vortexed for 30 seconds. Sample Preparation To make the study samples, aqueous humor (30 µL) was transferred from their original tubes into 2.0 mL Lo-Bind Eppendorf tubes. Six whole study pooled QC samples of 30 µL each were created along with three-30 µL time point A pool from right eye and three-30 µL time point A pool from left eye aqueous humor. For all samples (study, whole study pooled QC and time point A samples) 400 µL Protein Precipitation Buffer with internal standard (0.025 mg/mL of Tryptophan-d5 in methanol) was added to each tube and vortexed. The samples were then centrifuged at 16,000 rcf for 4 min. A 350 µL aliquot of the supernatant from each sample was transferred into pre-labeled 2.0 mL LoBind eppendorf tube and stored at -80 °C for one hour followed by a drying step on a lyophilizer. The residue was reconstituted in 100 µL of reconstitution buffer (95:5 Water:Methanol, v/v) and mixed on a multiple tube vortexer for 10 min at 5,000 rpm. Then, the samples were centrifuged at room temperature for 4 min at 16,000 rcf, and the supernatants were transferred to autosampler vials for data acquisition. |
| Sampleprep Protocol ID: | Protocol: RTI-RCMRC-LCMS-SA-018 Version: 1.0 |
| Sampleprep Protocol Filename: | 18 AP-Williamson-Aqueous humor-RTI-RCMRC-LCMS-SA-018_v1.0.docx |
| Processing Method: | Protein Precipitation followed by Metabolite Extraction and Lyophilization |
| Processing Storage Conditions: | On ice |
| Extraction Method: | Cold Methanol with Internal Standard |
| Extract Storage: | -80℃ |
| Sample Resuspension: | 95:5 Water:Methanol |
| Sample Spiking: | L-Tryptophan-d5 |
Combined analysis:
| Analysis ID | AN001523 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Waters Acquity |
| Column | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Waters Synapt-G2-Si |
| Ion Mode | POSITIVE |
| Units | Compound Normalised Abundance |
Chromatography:
| Chromatography ID: | CH001073 |
| Chromatography Summary: | Reversed-Phase Gradient Seperation |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters Acquity HSS T3 (100 x 2.1mm,1.8um) |
| Column Temperature: | 8 °C |
| Flow Gradient: | Time(min) Flow Rate(mL/min) %A %B Curve 1. Initial 0.400 99.0 1.0 2. 1.00 0.400 99.0 1.0 3. 16.00 0.400 1.0 99.0 4. 20.00 0.400 1.0 99.0 5. 20.50 0.400 99.0 1.0 6. 22.00 0.400 99.0 1.0 |
| Flow Rate: | 0.4 mL/min |
| Internal Standard: | L-Tryptophan-d5 |
| Solvent A: | 100% water; 0.1% formic acid |
| Solvent B: | 100% methanol; 0.1% formic acid |
| Analytical Time: | 22 min |
| Weak Wash Solvent Name: | 10% MeOH |
| Weak Wash Volume: | 1000 µL |
| Strong Wash Solvent Name: | 80% MeOH |
| Strong Wash Volume: | 1000 µL |
| Target Sample Temperature: | 8 °C |
| Sample Loop Size: | 10 µL |
| Sample Syringe Size: | 100 µL |
| Randomization Order: | Yes |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS001403 |
| Analysis ID: | AN001523 |
| Instrument Name: | Waters Synapt-G2-Si |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Capillary Temperature: | 110 °C |
| Capillary Voltage: | 1.0 kV |
| Collision Energy: | 4 |
| Fragmentation Method: | CID |
| Helium Flow: | 180 |
| Ionization: | ES+ |
| Mass Accuracy: | 5 ppm |
| Source Temperature: | 100 °C |
| Dataformat: | Continuum |
| Desolvation Gas Flow: | 400 L/Hr |
| Desolvation Temperature: | 400 °C |
| Resolution Setting: | 18000 |
| Scan Range Moverz: | 50-1000 m/z |
| Scanning Cycle: | 1.0 s |
| Tube Lens Voltage: | 75 |
